Multiple sequence alignment - TraesCS7D01G174800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G174800 chr7D 100.000 6685 0 0 1 6685 127024891 127018207 0.000000e+00 12345.0
1 TraesCS7D01G174800 chr7D 85.000 60 4 5 473 528 70695334 70695276 1.000000e-03 56.5
2 TraesCS7D01G174800 chr7D 100.000 28 0 0 555 582 528550238 528550211 1.200000e-02 52.8
3 TraesCS7D01G174800 chr7A 94.603 3743 134 32 587 4304 127829428 127825729 0.000000e+00 5731.0
4 TraesCS7D01G174800 chr7A 96.445 1322 46 1 4351 5671 127825731 127824410 0.000000e+00 2180.0
5 TraesCS7D01G174800 chr7A 93.833 600 33 4 1 597 127830196 127829598 0.000000e+00 900.0
6 TraesCS7D01G174800 chr7A 81.733 750 95 29 5913 6646 127824274 127823551 7.470000e-164 588.0
7 TraesCS7D01G174800 chr7A 86.087 115 5 2 5705 5808 127824408 127824294 5.480000e-21 113.0
8 TraesCS7D01G174800 chr7A 83.898 118 16 3 1241 1356 386588937 386588821 7.090000e-20 110.0
9 TraesCS7D01G174800 chr7B 94.320 2764 98 29 725 3458 88580136 88577402 0.000000e+00 4180.0
10 TraesCS7D01G174800 chr7B 94.248 2486 84 26 3770 6221 88577339 88574879 0.000000e+00 3744.0
11 TraesCS7D01G174800 chr7B 89.865 296 28 2 6392 6685 88574865 88574570 4.890000e-101 379.0
12 TraesCS7D01G174800 chr7B 95.833 48 1 1 3726 3772 88577402 88577355 7.190000e-10 76.8
13 TraesCS7D01G174800 chr2A 90.805 435 32 4 1687 2115 62532187 62531755 5.810000e-160 575.0
14 TraesCS7D01G174800 chr2B 89.976 409 34 3 1713 2115 662553813 662553406 7.680000e-144 521.0
15 TraesCS7D01G174800 chr3B 92.722 316 21 2 5341 5655 151836337 151836651 7.900000e-124 455.0
16 TraesCS7D01G174800 chr1B 79.242 501 77 15 2102 2595 69880943 69881423 2.330000e-84 324.0
17 TraesCS7D01G174800 chr1B 81.387 274 34 10 2841 3099 69881647 69881918 2.440000e-49 207.0
18 TraesCS7D01G174800 chr1D 85.556 90 9 1 2842 2927 49597110 49597199 2.570000e-14 91.6
19 TraesCS7D01G174800 chr6D 85.000 60 5 4 473 528 473350091 473350032 2.600000e-04 58.4
20 TraesCS7D01G174800 chr5D 100.000 30 0 0 553 582 390561653 390561682 1.000000e-03 56.5
21 TraesCS7D01G174800 chr5D 96.875 32 1 0 551 582 291532224 291532255 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G174800 chr7D 127018207 127024891 6684 True 12345.00 12345 100.0000 1 6685 1 chr7D.!!$R2 6684
1 TraesCS7D01G174800 chr7A 127823551 127830196 6645 True 1902.40 5731 90.5402 1 6646 5 chr7A.!!$R2 6645
2 TraesCS7D01G174800 chr7B 88574570 88580136 5566 True 2094.95 4180 93.5665 725 6685 4 chr7B.!!$R1 5960
3 TraesCS7D01G174800 chr1B 69880943 69881918 975 False 265.50 324 80.3145 2102 3099 2 chr1B.!!$F1 997

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
975 1176 0.188587 TCATCCTCTACCATCGCCCT 59.811 55.000 0.00 0.0 0.00 5.19 F
1340 1541 0.039035 TCTTCCATTGGTTTCCCCGG 59.961 55.000 1.86 0.0 35.15 5.73 F
2082 2330 0.040058 ATCCAATGCTGTTCTGGGCA 59.960 50.000 0.00 0.0 42.80 5.36 F
2333 2588 0.675633 CCAGTCCCAAGCTTTGTTGG 59.324 55.000 0.00 0.0 45.88 3.77 F
3502 3812 1.206849 GCTTCTAGCTCAAGCACTCCT 59.793 52.381 20.44 0.0 44.87 3.69 F
3796 4125 2.651382 GGTACCACACCCAAGAAGTT 57.349 50.000 7.15 0.0 42.07 2.66 F
5051 5381 0.109597 GTCGCTTGTTTGATGGCAGG 60.110 55.000 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2333 2588 1.168714 CTTCCCCACTGCTAAACTGC 58.831 55.000 0.00 0.0 0.00 4.40 R
3320 3630 4.100035 TCGACTGCAGAATACTGGATGAAT 59.900 41.667 23.35 0.0 43.07 2.57 R
3502 3812 1.202592 TGTGGAGAAAGCGTTGCAGTA 60.203 47.619 0.00 0.0 0.00 2.74 R
4213 4542 1.969923 GCCTCATAGGACTCATCTGCT 59.030 52.381 0.00 0.0 37.67 4.24 R
4821 5150 0.037303 AGGTTGGTGCAGAGATGGTG 59.963 55.000 0.00 0.0 0.00 4.17 R
5540 5870 0.680921 TATCAAGCCTGCAGTTGCCC 60.681 55.000 13.81 0.0 41.18 5.36 R
6326 6688 0.109132 CCGGGTTGCAGCTCATTTTC 60.109 55.000 0.00 0.0 0.00 2.29 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.814842 AGAAACATGCAGATTTGACGACA 59.185 39.130 2.85 0.00 0.00 4.35
58 59 1.587043 TTGACGACAGAGAGGGAGCG 61.587 60.000 0.00 0.00 0.00 5.03
80 81 2.068519 GTCAGATGACGCACACATTCA 58.931 47.619 0.00 0.00 35.12 2.57
87 88 1.131126 GACGCACACATTCAAGATGGG 59.869 52.381 0.00 0.00 0.00 4.00
122 123 3.304559 CACCGAGTCGAATCAAATCACTC 59.695 47.826 15.64 0.00 0.00 3.51
123 124 2.860735 CCGAGTCGAATCAAATCACTCC 59.139 50.000 15.64 0.00 31.49 3.85
144 145 2.889522 TATTAGGCCTCCCTGACCTT 57.110 50.000 9.68 0.00 42.90 3.50
168 169 1.879575 TCCGTGGGAAGGAATGAGAT 58.120 50.000 0.00 0.00 34.33 2.75
181 182 5.121811 AGGAATGAGATGAAAATGAGGTCG 58.878 41.667 0.00 0.00 0.00 4.79
183 184 3.333029 TGAGATGAAAATGAGGTCGCA 57.667 42.857 0.00 0.00 0.00 5.10
184 185 3.264947 TGAGATGAAAATGAGGTCGCAG 58.735 45.455 0.00 0.00 0.00 5.18
187 188 1.808411 TGAAAATGAGGTCGCAGGAC 58.192 50.000 0.00 0.00 42.66 3.85
225 226 4.539509 GTAGATGACGAGTCGACTCATT 57.460 45.455 37.14 26.55 43.00 2.57
250 251 2.312722 TTGCATGTGCTTTGTGCTTT 57.687 40.000 6.55 0.00 43.37 3.51
262 263 4.153475 GCTTTGTGCTTTGCATCATCATTT 59.847 37.500 0.00 0.00 41.91 2.32
289 290 4.953579 TGGTGGAAAACTAGTGCTTCTTTT 59.046 37.500 14.46 3.46 0.00 2.27
306 307 7.595502 TGCTTCTTTTCAAAACGTAAAAAGTCA 59.404 29.630 17.52 13.42 39.72 3.41
307 308 8.592155 GCTTCTTTTCAAAACGTAAAAAGTCAT 58.408 29.630 17.52 0.00 39.72 3.06
310 311 9.284594 TCTTTTCAAAACGTAAAAAGTCATCAG 57.715 29.630 17.52 0.00 39.72 2.90
318 319 8.428186 AACGTAAAAAGTCATCAGTTTAGTGA 57.572 30.769 0.00 0.00 0.00 3.41
363 366 8.734218 TTTTCTACATGTGTAACCACTTTGTA 57.266 30.769 9.11 0.00 42.34 2.41
373 376 8.240682 TGTGTAACCACTTTGTAATGCAATATC 58.759 33.333 0.00 0.00 42.34 1.63
399 402 6.097356 TCTTAGATTAGTGTGTTTACCGCAG 58.903 40.000 0.00 0.00 33.31 5.18
404 407 2.914059 AGTGTGTTTACCGCAGAGTTT 58.086 42.857 0.00 0.00 33.31 2.66
420 423 8.066595 CCGCAGAGTTTTTCTTTCATATATGAG 58.933 37.037 14.86 5.68 34.12 2.90
566 570 5.369699 ACCAGAGTTATAAGGGCATGTACAT 59.630 40.000 1.41 1.41 0.00 2.29
585 589 8.185506 TGTACATTAGTTGAGACACCTTCTAA 57.814 34.615 0.00 0.00 33.22 2.10
597 601 6.410540 AGACACCTTCTAAGAATGTGATTCC 58.589 40.000 11.65 0.44 34.52 3.01
598 602 6.013379 AGACACCTTCTAAGAATGTGATTCCA 60.013 38.462 11.65 0.00 34.52 3.53
599 603 5.940470 ACACCTTCTAAGAATGTGATTCCAC 59.060 40.000 12.35 0.00 43.46 4.02
600 604 5.063944 CACCTTCTAAGAATGTGATTCCACG 59.936 44.000 0.00 0.00 46.06 4.94
601 605 5.046591 ACCTTCTAAGAATGTGATTCCACGA 60.047 40.000 0.00 0.00 46.06 4.35
602 606 5.292101 CCTTCTAAGAATGTGATTCCACGAC 59.708 44.000 0.00 0.00 46.06 4.34
604 608 2.010145 AGAATGTGATTCCACGACGG 57.990 50.000 0.00 0.00 46.06 4.79
605 609 0.373716 GAATGTGATTCCACGACGGC 59.626 55.000 0.00 0.00 46.06 5.68
606 610 1.358725 AATGTGATTCCACGACGGCG 61.359 55.000 10.39 10.39 46.06 6.46
607 611 2.126228 GTGATTCCACGACGGCGA 60.126 61.111 22.49 0.00 41.64 5.54
608 612 1.518572 GTGATTCCACGACGGCGAT 60.519 57.895 22.49 0.00 41.64 4.58
609 613 1.518352 TGATTCCACGACGGCGATG 60.518 57.895 22.49 12.48 41.64 3.84
610 614 1.518572 GATTCCACGACGGCGATGT 60.519 57.895 22.49 8.65 41.64 3.06
611 615 1.752501 GATTCCACGACGGCGATGTG 61.753 60.000 22.49 20.55 41.64 3.21
637 815 1.001048 CGTCCGAGAAGGTGTTGTGTA 60.001 52.381 0.00 0.00 41.99 2.90
656 834 6.688578 TGTGTACATCTCTCAAAAGTAGACC 58.311 40.000 0.00 0.00 30.57 3.85
867 1049 2.416893 GGTCTTGCTCATTTCGTTCCTC 59.583 50.000 0.00 0.00 0.00 3.71
968 1169 2.495084 CGTCGAGATCATCCTCTACCA 58.505 52.381 0.00 0.00 0.00 3.25
969 1170 3.078097 CGTCGAGATCATCCTCTACCAT 58.922 50.000 0.00 0.00 0.00 3.55
970 1171 3.126171 CGTCGAGATCATCCTCTACCATC 59.874 52.174 0.00 0.00 0.00 3.51
971 1172 3.126171 GTCGAGATCATCCTCTACCATCG 59.874 52.174 0.00 0.00 0.00 3.84
972 1173 2.159448 CGAGATCATCCTCTACCATCGC 60.159 54.545 0.00 0.00 0.00 4.58
974 1175 1.205893 GATCATCCTCTACCATCGCCC 59.794 57.143 0.00 0.00 0.00 6.13
975 1176 0.188587 TCATCCTCTACCATCGCCCT 59.811 55.000 0.00 0.00 0.00 5.19
976 1177 1.427753 TCATCCTCTACCATCGCCCTA 59.572 52.381 0.00 0.00 0.00 3.53
1016 1217 1.276421 TCCTGCTTAGTGACTTGCTCC 59.724 52.381 10.61 0.00 0.00 4.70
1096 1297 2.638154 CGTCTATCTCGACCCGGC 59.362 66.667 0.00 0.00 0.00 6.13
1337 1538 2.604139 TGGTTCTTCCATTGGTTTCCC 58.396 47.619 1.86 0.00 41.93 3.97
1338 1539 1.899814 GGTTCTTCCATTGGTTTCCCC 59.100 52.381 1.86 0.00 35.97 4.81
1339 1540 1.544246 GTTCTTCCATTGGTTTCCCCG 59.456 52.381 1.86 0.00 35.15 5.73
1340 1541 0.039035 TCTTCCATTGGTTTCCCCGG 59.961 55.000 1.86 0.00 35.15 5.73
1341 1542 0.970427 CTTCCATTGGTTTCCCCGGG 60.970 60.000 15.80 15.80 35.15 5.73
1342 1543 2.363665 CCATTGGTTTCCCCGGGG 60.364 66.667 35.80 35.80 35.15 5.73
1343 1544 2.363665 CATTGGTTTCCCCGGGGG 60.364 66.667 39.51 27.32 46.11 5.40
1344 1545 4.392166 ATTGGTTTCCCCGGGGGC 62.392 66.667 39.51 27.23 43.94 5.80
1346 1547 4.679003 TGGTTTCCCCGGGGGCTA 62.679 66.667 39.51 23.58 43.94 3.93
1347 1548 3.340782 GGTTTCCCCGGGGGCTAA 61.341 66.667 39.51 26.27 43.94 3.09
1348 1549 2.697022 GGTTTCCCCGGGGGCTAAT 61.697 63.158 39.51 0.00 43.94 1.73
1349 1550 1.308666 GTTTCCCCGGGGGCTAATT 59.691 57.895 39.51 0.00 43.94 1.40
1350 1551 1.040893 GTTTCCCCGGGGGCTAATTG 61.041 60.000 39.51 11.60 43.94 2.32
1351 1552 2.231540 TTTCCCCGGGGGCTAATTGG 62.232 60.000 39.51 10.77 43.94 3.16
1352 1553 3.425925 CCCCGGGGGCTAATTGGT 61.426 66.667 34.01 0.00 35.35 3.67
1353 1554 2.194868 CCCGGGGGCTAATTGGTC 59.805 66.667 14.71 0.00 0.00 4.02
1461 1697 3.891049 CCTTCCTCTGGGAACTAATTGG 58.109 50.000 0.00 0.00 45.72 3.16
1473 1709 3.282831 ACTAATTGGTTGCGTTCTTGC 57.717 42.857 0.00 0.00 0.00 4.01
1482 1718 1.234821 TGCGTTCTTGCTCGGATTTT 58.765 45.000 0.00 0.00 35.36 1.82
1486 1722 1.978782 GTTCTTGCTCGGATTTTTGCG 59.021 47.619 0.00 0.00 0.00 4.85
1574 1816 1.420138 TGGTTCTTTCACCTCTCACCC 59.580 52.381 0.00 0.00 37.75 4.61
1577 1819 1.352083 TCTTTCACCTCTCACCCAGG 58.648 55.000 0.00 0.00 37.03 4.45
1592 1834 2.310538 CCCAGGGCTAATTTGGTGATC 58.689 52.381 0.00 0.00 0.00 2.92
1600 1842 4.158394 GGCTAATTTGGTGATCTTCTTGCA 59.842 41.667 0.00 0.00 0.00 4.08
1626 1868 6.855836 TGATTCTTGCAATGTGTTTATCTCC 58.144 36.000 0.00 0.00 0.00 3.71
2078 2326 8.081633 TGTTAAGTTTTATCCAATGCTGTTCTG 58.918 33.333 0.00 0.00 0.00 3.02
2082 2330 0.040058 ATCCAATGCTGTTCTGGGCA 59.960 50.000 0.00 0.00 42.80 5.36
2130 2379 7.674471 AAGAGAGCACCTTTTTATGTCTAAC 57.326 36.000 0.00 0.00 0.00 2.34
2144 2393 9.635404 TTTTATGTCTAACTCTTTTCCTGGAAA 57.365 29.630 17.65 17.65 0.00 3.13
2157 2407 3.122480 TCCTGGAAATTCCTATGCTGGA 58.878 45.455 13.78 8.11 37.46 3.86
2333 2588 0.675633 CCAGTCCCAAGCTTTGTTGG 59.324 55.000 0.00 0.00 45.88 3.77
2403 2658 6.844388 AGGATATGGACAGTACAGGATTAACA 59.156 38.462 0.00 0.00 0.00 2.41
2429 2684 6.421377 AAAATTGCTTTGAGAAAACACACC 57.579 33.333 0.00 0.00 0.00 4.16
3200 3510 4.513318 TGATGCGTACAATCTTTTGTGACA 59.487 37.500 1.76 0.00 45.56 3.58
3201 3511 4.884458 TGCGTACAATCTTTTGTGACAA 57.116 36.364 0.00 0.00 45.56 3.18
3341 3651 7.572724 GCATAATTCATCCAGTATTCTGCAGTC 60.573 40.741 14.67 3.42 37.19 3.51
3391 3701 7.881142 CAGTATGCTCTAGCTAAGTTCTATGT 58.119 38.462 3.26 0.00 42.66 2.29
3408 3718 7.721399 AGTTCTATGTTTTGGTTCTGTCTGAAT 59.279 33.333 0.00 0.00 36.99 2.57
3419 3729 7.453393 TGGTTCTGTCTGAATAATGTCTTTCT 58.547 34.615 0.00 0.00 36.99 2.52
3502 3812 1.206849 GCTTCTAGCTCAAGCACTCCT 59.793 52.381 20.44 0.00 44.87 3.69
3551 3861 8.548877 AGGAAGATGGTTAGTAAATGCTTTCTA 58.451 33.333 0.00 0.00 0.00 2.10
3669 3979 4.725754 CGCTTAATCGAACATCTGCTTTTC 59.274 41.667 0.00 0.00 0.00 2.29
3796 4125 2.651382 GGTACCACACCCAAGAAGTT 57.349 50.000 7.15 0.00 42.07 2.66
4091 4420 6.027749 CCACCAAAATACGCTATTCAACTTC 58.972 40.000 0.00 0.00 0.00 3.01
4213 4542 4.022676 TGAATACGCGATCAAGCCATAGTA 60.023 41.667 15.93 0.00 0.00 1.82
4451 4780 5.753921 GGAGTAGAACATATTTCCGTTCCAG 59.246 44.000 0.00 0.00 42.00 3.86
4598 4927 5.503357 GCAACTGATTACGTTGTTTCTGTGA 60.503 40.000 0.00 0.00 42.73 3.58
4621 4950 9.495754 GTGATTTCTGTTGCAATACTCTAATTC 57.504 33.333 0.59 0.00 0.00 2.17
4821 5150 1.339055 TGGTACACCTGCAATGAGAGC 60.339 52.381 4.68 3.05 36.82 4.09
4943 5273 2.945668 GGAAGGTAGACATGCATGAACC 59.054 50.000 32.75 29.83 0.00 3.62
5051 5381 0.109597 GTCGCTTGTTTGATGGCAGG 60.110 55.000 0.00 0.00 0.00 4.85
5082 5412 0.537143 CAGGTGCTGCAGGGTTGTTA 60.537 55.000 17.12 0.00 0.00 2.41
5237 5567 1.001406 GCTGGAGTCCCATCTATTCCG 59.999 57.143 6.74 0.00 42.59 4.30
5480 5810 7.154435 TCAGTCATGTTAGTTACTCTGGTAC 57.846 40.000 0.00 0.00 0.00 3.34
5540 5870 7.271511 AGAAAGAGATGGTAAATGCTGTAGAG 58.728 38.462 0.00 0.00 0.00 2.43
5633 5963 0.169009 GCATTCTTTCAGTGCCCGTC 59.831 55.000 0.00 0.00 32.88 4.79
5671 6001 2.744318 TGTGCCCGCAATGGTACG 60.744 61.111 0.00 0.00 43.22 3.67
5688 6018 5.157781 TGGTACGCTTTTGTTATGAATTGC 58.842 37.500 0.00 0.00 0.00 3.56
5689 6019 5.157781 GGTACGCTTTTGTTATGAATTGCA 58.842 37.500 0.00 0.00 0.00 4.08
5741 6075 1.001293 TGCTAGTTCTGAGTGCTGTGG 59.999 52.381 0.00 0.00 0.00 4.17
5757 6091 4.700692 TGCTGTGGTGTAAACTTGTGTAAA 59.299 37.500 0.00 0.00 0.00 2.01
5816 6168 6.803154 AAGGATTTCAGTTTCGGTTCTTAG 57.197 37.500 0.00 0.00 0.00 2.18
5826 6178 7.935210 TCAGTTTCGGTTCTTAGGTAATCTTTT 59.065 33.333 0.00 0.00 0.00 2.27
5861 6213 0.804364 TCTGCATACTGCTTTTGCCG 59.196 50.000 0.34 0.00 45.31 5.69
5878 6230 1.873486 GCCGCATTTTTCCTGCTTGTT 60.873 47.619 0.00 0.00 37.48 2.83
5946 6298 6.309494 CAGTTCATGCTACATTTGTTTGGATG 59.691 38.462 9.74 9.74 33.81 3.51
5948 6300 5.712004 TCATGCTACATTTGTTTGGATGTG 58.288 37.500 13.23 0.00 37.12 3.21
5949 6301 4.517952 TGCTACATTTGTTTGGATGTGG 57.482 40.909 0.00 0.00 37.12 4.17
5950 6302 3.894427 TGCTACATTTGTTTGGATGTGGT 59.106 39.130 0.00 0.00 37.16 4.16
6034 6390 1.133668 ACTTCTTGCCCTTCTGCAGTT 60.134 47.619 14.67 0.00 43.21 3.16
6046 6402 6.122277 CCCTTCTGCAGTTCAATATCCTTTA 58.878 40.000 14.67 0.00 0.00 1.85
6166 6527 9.816354 TTTAAAGCAGAAAATTGAAAAGCTACT 57.184 25.926 0.00 0.00 0.00 2.57
6209 6571 2.586792 AGCCGACAAGCTCCATCC 59.413 61.111 0.00 0.00 39.48 3.51
6211 6573 1.078143 GCCGACAAGCTCCATCCTT 60.078 57.895 0.00 0.00 0.00 3.36
6212 6574 0.678048 GCCGACAAGCTCCATCCTTT 60.678 55.000 0.00 0.00 0.00 3.11
6213 6575 1.406887 GCCGACAAGCTCCATCCTTTA 60.407 52.381 0.00 0.00 0.00 1.85
6214 6576 2.280628 CCGACAAGCTCCATCCTTTAC 58.719 52.381 0.00 0.00 0.00 2.01
6215 6577 2.354704 CCGACAAGCTCCATCCTTTACA 60.355 50.000 0.00 0.00 0.00 2.41
6216 6578 3.535561 CGACAAGCTCCATCCTTTACAT 58.464 45.455 0.00 0.00 0.00 2.29
6217 6579 4.442893 CCGACAAGCTCCATCCTTTACATA 60.443 45.833 0.00 0.00 0.00 2.29
6218 6580 4.508124 CGACAAGCTCCATCCTTTACATAC 59.492 45.833 0.00 0.00 0.00 2.39
6219 6581 5.428253 GACAAGCTCCATCCTTTACATACA 58.572 41.667 0.00 0.00 0.00 2.29
6221 6583 5.045578 ACAAGCTCCATCCTTTACATACAGT 60.046 40.000 0.00 0.00 0.00 3.55
6222 6584 5.700402 AGCTCCATCCTTTACATACAGTT 57.300 39.130 0.00 0.00 0.00 3.16
6223 6585 6.808321 AGCTCCATCCTTTACATACAGTTA 57.192 37.500 0.00 0.00 0.00 2.24
6229 6591 7.343574 TCCATCCTTTACATACAGTTACAGCTA 59.656 37.037 0.00 0.00 0.00 3.32
6241 6603 7.900782 ACAGTTACAGCTATTTGTTATTCGT 57.099 32.000 0.00 0.00 32.56 3.85
6249 6611 7.985184 ACAGCTATTTGTTATTCGTATGGAAGA 59.015 33.333 0.00 0.00 38.24 2.87
6260 6622 5.786264 TCGTATGGAAGAATCTTAGACCC 57.214 43.478 0.00 0.00 0.00 4.46
6261 6623 5.455872 TCGTATGGAAGAATCTTAGACCCT 58.544 41.667 0.00 0.00 0.00 4.34
6266 6628 4.844085 TGGAAGAATCTTAGACCCTGTTCA 59.156 41.667 0.00 0.00 0.00 3.18
6268 6630 5.187967 GGAAGAATCTTAGACCCTGTTCAGA 59.812 44.000 0.00 0.00 0.00 3.27
6269 6631 6.295916 GGAAGAATCTTAGACCCTGTTCAGAA 60.296 42.308 0.00 0.00 0.00 3.02
6272 6634 6.671779 AGAATCTTAGACCCTGTTCAGAATCT 59.328 38.462 1.00 6.28 0.00 2.40
6276 6638 3.784178 AGACCCTGTTCAGAATCTCTCA 58.216 45.455 1.00 0.00 0.00 3.27
6277 6639 4.360889 AGACCCTGTTCAGAATCTCTCAT 58.639 43.478 1.00 0.00 0.00 2.90
6282 6644 4.499526 CCTGTTCAGAATCTCTCATCTCCG 60.500 50.000 1.00 0.00 0.00 4.63
6283 6645 3.181482 TGTTCAGAATCTCTCATCTCCGC 60.181 47.826 0.00 0.00 0.00 5.54
6284 6646 2.942804 TCAGAATCTCTCATCTCCGCT 58.057 47.619 0.00 0.00 0.00 5.52
6285 6647 2.884012 TCAGAATCTCTCATCTCCGCTC 59.116 50.000 0.00 0.00 0.00 5.03
6286 6648 1.879380 AGAATCTCTCATCTCCGCTCG 59.121 52.381 0.00 0.00 0.00 5.03
6287 6649 1.876799 GAATCTCTCATCTCCGCTCGA 59.123 52.381 0.00 0.00 0.00 4.04
6289 6651 0.179234 TCTCTCATCTCCGCTCGACT 59.821 55.000 0.00 0.00 0.00 4.18
6290 6652 0.586319 CTCTCATCTCCGCTCGACTC 59.414 60.000 0.00 0.00 0.00 3.36
6291 6653 0.816018 TCTCATCTCCGCTCGACTCC 60.816 60.000 0.00 0.00 0.00 3.85
6292 6654 2.111932 CTCATCTCCGCTCGACTCCG 62.112 65.000 0.00 0.00 37.07 4.63
6317 6679 1.466558 GCTGTGGAGCTCTGTTTTAGC 59.533 52.381 14.64 11.14 42.52 3.09
6318 6680 2.079925 CTGTGGAGCTCTGTTTTAGCC 58.920 52.381 14.64 0.00 41.02 3.93
6319 6681 1.079503 GTGGAGCTCTGTTTTAGCCG 58.920 55.000 14.64 0.00 41.02 5.52
6320 6682 0.673644 TGGAGCTCTGTTTTAGCCGC 60.674 55.000 14.64 0.00 41.02 6.53
6321 6683 0.391793 GGAGCTCTGTTTTAGCCGCT 60.392 55.000 14.64 0.00 41.02 5.52
6323 6685 0.391793 AGCTCTGTTTTAGCCGCTCC 60.392 55.000 0.00 0.00 41.02 4.70
6325 6687 0.389948 CTCTGTTTTAGCCGCTCCGT 60.390 55.000 0.00 0.00 0.00 4.69
6326 6688 0.669318 TCTGTTTTAGCCGCTCCGTG 60.669 55.000 0.00 0.00 0.00 4.94
6329 6691 0.869730 GTTTTAGCCGCTCCGTGAAA 59.130 50.000 0.00 0.00 0.00 2.69
6331 6693 1.816074 TTTAGCCGCTCCGTGAAAAT 58.184 45.000 0.00 0.00 0.00 1.82
6332 6694 1.083489 TTAGCCGCTCCGTGAAAATG 58.917 50.000 0.00 0.00 0.00 2.32
6333 6695 0.248012 TAGCCGCTCCGTGAAAATGA 59.752 50.000 0.00 0.00 0.00 2.57
6334 6696 1.021390 AGCCGCTCCGTGAAAATGAG 61.021 55.000 0.00 0.00 0.00 2.90
6337 6699 3.984292 GCTCCGTGAAAATGAGCTG 57.016 52.632 0.00 0.00 46.19 4.24
6339 6701 1.159285 CTCCGTGAAAATGAGCTGCA 58.841 50.000 1.02 0.00 0.00 4.41
6340 6702 1.536766 CTCCGTGAAAATGAGCTGCAA 59.463 47.619 1.02 0.00 0.00 4.08
6341 6703 1.266718 TCCGTGAAAATGAGCTGCAAC 59.733 47.619 1.02 0.00 0.00 4.17
6342 6704 1.666888 CCGTGAAAATGAGCTGCAACC 60.667 52.381 1.02 0.00 0.00 3.77
6343 6705 1.666888 CGTGAAAATGAGCTGCAACCC 60.667 52.381 1.02 0.00 0.00 4.11
6344 6706 0.597568 TGAAAATGAGCTGCAACCCG 59.402 50.000 1.02 0.00 0.00 5.28
6345 6707 0.109132 GAAAATGAGCTGCAACCCGG 60.109 55.000 1.02 0.00 0.00 5.73
6346 6708 0.827507 AAAATGAGCTGCAACCCGGT 60.828 50.000 0.00 0.00 0.00 5.28
6347 6709 1.244019 AAATGAGCTGCAACCCGGTC 61.244 55.000 0.00 0.00 0.00 4.79
6348 6710 3.628646 ATGAGCTGCAACCCGGTCC 62.629 63.158 0.00 0.00 0.00 4.46
6370 6732 0.250234 TCCGGAGCACAATTGAGGAG 59.750 55.000 13.59 0.13 0.00 3.69
6371 6733 1.372087 CCGGAGCACAATTGAGGAGC 61.372 60.000 13.59 10.25 0.00 4.70
6373 6735 1.372087 GGAGCACAATTGAGGAGCGG 61.372 60.000 13.59 0.00 0.00 5.52
6374 6736 0.391661 GAGCACAATTGAGGAGCGGA 60.392 55.000 13.59 0.00 0.00 5.54
6377 6739 1.649664 CACAATTGAGGAGCGGAGAG 58.350 55.000 13.59 0.00 0.00 3.20
6378 6740 0.539051 ACAATTGAGGAGCGGAGAGG 59.461 55.000 13.59 0.00 0.00 3.69
6379 6741 0.826715 CAATTGAGGAGCGGAGAGGA 59.173 55.000 0.00 0.00 0.00 3.71
6380 6742 1.208052 CAATTGAGGAGCGGAGAGGAA 59.792 52.381 0.00 0.00 0.00 3.36
6381 6743 0.827368 ATTGAGGAGCGGAGAGGAAC 59.173 55.000 0.00 0.00 0.00 3.62
6382 6744 1.258445 TTGAGGAGCGGAGAGGAACC 61.258 60.000 0.00 0.00 0.00 3.62
6389 6751 2.577593 GGAGAGGAACCGAACGGG 59.422 66.667 17.44 0.00 43.62 5.28
6390 6752 2.125633 GAGAGGAACCGAACGGGC 60.126 66.667 17.44 8.71 40.62 6.13
6391 6753 2.603776 AGAGGAACCGAACGGGCT 60.604 61.111 17.44 4.12 40.62 5.19
6398 6760 1.474077 GAACCGAACGGGCTCTTAGTA 59.526 52.381 17.44 0.00 40.62 1.82
6404 6766 3.243771 CGAACGGGCTCTTAGTATGGAAT 60.244 47.826 0.00 0.00 0.00 3.01
6422 6784 4.459685 TGGAATAGTAGAGCTCGAATAGGC 59.540 45.833 8.37 3.17 0.00 3.93
6502 6866 4.521639 TGCTTGCTTGTTCTCTGAATTGAT 59.478 37.500 0.00 0.00 0.00 2.57
6524 6888 4.308899 AGTTGCTACTACGGATGATGAC 57.691 45.455 0.00 0.00 31.21 3.06
6537 6901 1.275666 TGATGACGTTGATGGGGACT 58.724 50.000 0.00 0.00 0.00 3.85
6654 7019 3.610677 GGAAGTTTTGTGAACGTTTGGTG 59.389 43.478 0.46 0.00 0.00 4.17
6655 7020 4.477780 GAAGTTTTGTGAACGTTTGGTGA 58.522 39.130 0.46 0.00 0.00 4.02
6673 7038 2.875933 GTGATCGTTGAAAGACCAACCA 59.124 45.455 0.00 0.00 42.42 3.67
6674 7039 2.875933 TGATCGTTGAAAGACCAACCAC 59.124 45.455 0.00 0.00 42.42 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 2.902423 ATCTGACGCGCTCCCTCTCT 62.902 60.000 5.73 0.00 0.00 3.10
80 81 1.302511 GTGTCACGGTGCCCATCTT 60.303 57.895 2.51 0.00 0.00 2.40
101 102 3.512680 GAGTGATTTGATTCGACTCGGT 58.487 45.455 0.00 0.00 0.00 4.69
122 123 1.630878 GGTCAGGGAGGCCTAATATGG 59.369 57.143 4.42 0.00 39.61 2.74
144 145 1.065491 CATTCCTTCCCACGGATGTCA 60.065 52.381 0.00 0.00 0.00 3.58
168 169 1.808411 GTCCTGCGACCTCATTTTCA 58.192 50.000 0.00 0.00 32.40 2.69
181 182 2.027561 TGTGGTAGTGTAATGGTCCTGC 60.028 50.000 0.00 0.00 0.00 4.85
183 184 2.232941 CGTGTGGTAGTGTAATGGTCCT 59.767 50.000 0.00 0.00 0.00 3.85
184 185 2.028748 ACGTGTGGTAGTGTAATGGTCC 60.029 50.000 0.00 0.00 0.00 4.46
215 216 6.358030 GCACATGCAATATTTAATGAGTCGAC 59.642 38.462 7.70 7.70 41.59 4.20
216 217 6.260714 AGCACATGCAATATTTAATGAGTCGA 59.739 34.615 6.64 0.00 45.16 4.20
250 251 4.024670 TCCACCATGAAAATGATGATGCA 58.975 39.130 0.00 0.00 0.00 3.96
262 263 4.098914 AGCACTAGTTTTCCACCATGAA 57.901 40.909 0.00 0.00 0.00 2.57
289 290 9.710979 CTAAACTGATGACTTTTTACGTTTTGA 57.289 29.630 0.00 0.00 0.00 2.69
373 376 6.533723 TGCGGTAAACACACTAATCTAAGATG 59.466 38.462 0.00 0.00 0.00 2.90
384 387 2.614829 AACTCTGCGGTAAACACACT 57.385 45.000 0.00 0.00 0.00 3.55
566 570 7.872993 CACATTCTTAGAAGGTGTCTCAACTAA 59.127 37.037 25.64 0.00 37.84 2.24
585 589 2.007049 GCCGTCGTGGAATCACATTCT 61.007 52.381 0.51 0.00 43.79 2.40
623 801 4.588951 TGAGAGATGTACACAACACCTTCT 59.411 41.667 0.00 0.00 42.09 2.85
637 815 5.645497 GCATTGGTCTACTTTTGAGAGATGT 59.355 40.000 0.00 0.00 0.00 3.06
844 1026 1.128692 GAACGAAATGAGCAAGACCGG 59.871 52.381 0.00 0.00 0.00 5.28
972 1173 3.222121 GTAGCGACGGGGGTAGGG 61.222 72.222 0.00 0.00 0.00 3.53
974 1175 2.440796 TGGTAGCGACGGGGGTAG 60.441 66.667 0.00 0.00 0.00 3.18
975 1176 2.755469 GTGGTAGCGACGGGGGTA 60.755 66.667 0.00 0.00 0.00 3.69
988 1189 3.073062 AGTCACTAAGCAGGAAATGTGGT 59.927 43.478 0.00 0.00 0.00 4.16
1290 1491 4.213564 AGAATCAGAGCAAGGTCGAAAT 57.786 40.909 0.00 0.00 0.00 2.17
1336 1537 2.194868 GACCAATTAGCCCCCGGG 59.805 66.667 15.80 15.80 38.57 5.73
1337 1538 2.194868 GGACCAATTAGCCCCCGG 59.805 66.667 0.00 0.00 0.00 5.73
1338 1539 2.194868 GGGACCAATTAGCCCCCG 59.805 66.667 0.00 0.00 35.76 5.73
1339 1540 2.194868 CGGGACCAATTAGCCCCC 59.805 66.667 0.00 0.00 38.69 5.40
1340 1541 0.750546 GAACGGGACCAATTAGCCCC 60.751 60.000 0.00 0.00 38.69 5.80
1341 1542 0.255033 AGAACGGGACCAATTAGCCC 59.745 55.000 0.00 0.00 38.53 5.19
1342 1543 1.743394 CAAGAACGGGACCAATTAGCC 59.257 52.381 0.00 0.00 0.00 3.93
1343 1544 1.132453 GCAAGAACGGGACCAATTAGC 59.868 52.381 0.00 0.00 0.00 3.09
1344 1545 2.678336 GAGCAAGAACGGGACCAATTAG 59.322 50.000 0.00 0.00 0.00 1.73
1345 1546 2.039216 TGAGCAAGAACGGGACCAATTA 59.961 45.455 0.00 0.00 0.00 1.40
1346 1547 1.202879 TGAGCAAGAACGGGACCAATT 60.203 47.619 0.00 0.00 0.00 2.32
1347 1548 0.400213 TGAGCAAGAACGGGACCAAT 59.600 50.000 0.00 0.00 0.00 3.16
1348 1549 0.250295 CTGAGCAAGAACGGGACCAA 60.250 55.000 0.00 0.00 0.00 3.67
1349 1550 1.118965 TCTGAGCAAGAACGGGACCA 61.119 55.000 0.00 0.00 29.54 4.02
1350 1551 0.250513 ATCTGAGCAAGAACGGGACC 59.749 55.000 0.00 0.00 38.79 4.46
1351 1552 2.003301 GAATCTGAGCAAGAACGGGAC 58.997 52.381 0.00 0.00 38.79 4.46
1352 1553 1.902508 AGAATCTGAGCAAGAACGGGA 59.097 47.619 0.00 0.00 38.79 5.14
1353 1554 2.393271 AGAATCTGAGCAAGAACGGG 57.607 50.000 0.00 0.00 38.79 5.28
1452 1687 3.317993 AGCAAGAACGCAACCAATTAGTT 59.682 39.130 0.00 0.00 0.00 2.24
1461 1697 0.517316 AATCCGAGCAAGAACGCAAC 59.483 50.000 0.00 0.00 0.00 4.17
1473 1709 0.240945 AACCAGCGCAAAAATCCGAG 59.759 50.000 11.47 0.00 0.00 4.63
1486 1722 0.799393 GAGGAAGCGAAAGAACCAGC 59.201 55.000 0.00 0.00 0.00 4.85
1574 1816 4.530875 AGAAGATCACCAAATTAGCCCTG 58.469 43.478 0.00 0.00 0.00 4.45
1577 1819 4.158394 TGCAAGAAGATCACCAAATTAGCC 59.842 41.667 0.00 0.00 0.00 3.93
1600 1842 7.362401 GGAGATAAACACATTGCAAGAATCAGT 60.362 37.037 4.94 0.00 0.00 3.41
2078 2326 5.185828 AGACTGAACCAAATCTTTTATGCCC 59.814 40.000 0.00 0.00 0.00 5.36
2130 2379 5.890419 AGCATAGGAATTTCCAGGAAAAGAG 59.110 40.000 18.88 6.20 39.61 2.85
2144 2393 4.032310 TGCCATTTTTCCAGCATAGGAAT 58.968 39.130 6.19 0.00 46.45 3.01
2157 2407 2.738139 GCGCGCCTTGCCATTTTT 60.738 55.556 23.24 0.00 42.08 1.94
2333 2588 1.168714 CTTCCCCACTGCTAAACTGC 58.831 55.000 0.00 0.00 0.00 4.40
3023 3331 9.435688 AGAAAAATGATAATAAAACAGGCCAAC 57.564 29.630 5.01 0.00 0.00 3.77
3271 3581 8.088365 ACTTTGGTTTCTATTAGCAAATGTTCC 58.912 33.333 0.00 0.00 40.79 3.62
3317 3627 6.648310 CGACTGCAGAATACTGGATGAATTAT 59.352 38.462 23.35 0.00 43.07 1.28
3320 3630 4.100035 TCGACTGCAGAATACTGGATGAAT 59.900 41.667 23.35 0.00 43.07 2.57
3325 3635 5.768164 TGTATATCGACTGCAGAATACTGGA 59.232 40.000 23.35 4.41 43.62 3.86
3341 3651 5.338822 CCAGTTTCATCGTACGTGTATATCG 59.661 44.000 16.05 0.12 0.00 2.92
3391 3701 8.463930 AAGACATTATTCAGACAGAACCAAAA 57.536 30.769 0.00 0.00 39.49 2.44
3419 3729 8.587608 TGCACACAGATGATATGATGATAAGTA 58.412 33.333 0.00 0.00 0.00 2.24
3502 3812 1.202592 TGTGGAGAAAGCGTTGCAGTA 60.203 47.619 0.00 0.00 0.00 2.74
3669 3979 3.005554 CTGAAGTATGAGTTGCCCAGTG 58.994 50.000 0.00 0.00 0.00 3.66
4213 4542 1.969923 GCCTCATAGGACTCATCTGCT 59.030 52.381 0.00 0.00 37.67 4.24
4341 4670 8.601546 AGTTGGATCCCTTTTAATAATTTGCAA 58.398 29.630 9.90 0.00 0.00 4.08
4427 4756 5.667466 TGGAACGGAAATATGTTCTACTCC 58.333 41.667 5.24 0.00 43.10 3.85
4451 4780 9.457110 CAGTAGCATCTTATATTCGTCCATATC 57.543 37.037 0.00 0.00 0.00 1.63
4646 4975 4.987408 ATACAAATACTGCTGCAATGCA 57.013 36.364 7.99 7.99 41.05 3.96
4821 5150 0.037303 AGGTTGGTGCAGAGATGGTG 59.963 55.000 0.00 0.00 0.00 4.17
4943 5273 4.201792 GCAGCACTGAAATATGACACAGAG 60.202 45.833 0.81 0.00 34.88 3.35
5051 5381 4.261888 CACCTGTAGTGCCGTCAC 57.738 61.111 0.00 0.00 40.28 3.67
5082 5412 1.202879 TGCCACGTTTCCCTCTTGATT 60.203 47.619 0.00 0.00 0.00 2.57
5480 5810 4.739228 CAGTAGTCTGCGAATCATTCTCTG 59.261 45.833 0.00 0.00 34.79 3.35
5524 5854 1.912731 TGCCCTCTACAGCATTTACCA 59.087 47.619 0.00 0.00 33.08 3.25
5540 5870 0.680921 TATCAAGCCTGCAGTTGCCC 60.681 55.000 13.81 0.00 41.18 5.36
5594 5924 2.805099 GCTATTCAGCTGCATCTACACC 59.195 50.000 9.47 0.00 44.93 4.16
5603 5933 4.599047 CTGAAAGAATGCTATTCAGCTGC 58.401 43.478 9.47 0.00 42.76 5.25
5633 5963 1.886542 GCTACCTGTGTTTTTCCCCAG 59.113 52.381 0.00 0.00 0.00 4.45
5671 6001 4.632688 AGCCATGCAATTCATAACAAAAGC 59.367 37.500 0.00 0.00 33.19 3.51
5688 6018 5.126396 TCATCGACAAGATAGTAGCCATG 57.874 43.478 0.00 0.00 37.52 3.66
5689 6019 5.303078 AGTTCATCGACAAGATAGTAGCCAT 59.697 40.000 0.00 0.00 37.52 4.40
5741 6075 6.432936 GCCCTACTTTTACACAAGTTTACAC 58.567 40.000 0.00 0.00 38.07 2.90
5757 6091 0.916358 ATCAGTGCCTGGCCCTACTT 60.916 55.000 17.53 0.00 31.51 2.24
5787 6136 7.665974 AGAACCGAAACTGAAATCCTTTCTATT 59.334 33.333 1.74 0.00 40.32 1.73
5852 6204 1.195222 CAGGAAAAATGCGGCAAAAGC 59.805 47.619 6.82 0.00 0.00 3.51
5854 6206 1.224965 GCAGGAAAAATGCGGCAAAA 58.775 45.000 6.82 0.00 33.31 2.44
5861 6213 2.955607 GCAACAAGCAGGAAAAATGC 57.044 45.000 0.00 0.00 44.79 3.56
5878 6230 2.158856 TGCCAATTTTCCACAACATGCA 60.159 40.909 0.00 0.00 0.00 3.96
5887 6239 2.103941 GGTTTCTGGTGCCAATTTTCCA 59.896 45.455 0.00 0.00 0.00 3.53
5946 6298 3.756963 GACCTTCAAAATCCTACCACCAC 59.243 47.826 0.00 0.00 0.00 4.16
5948 6300 4.028993 TGACCTTCAAAATCCTACCACC 57.971 45.455 0.00 0.00 0.00 4.61
5949 6301 4.459337 CCTTGACCTTCAAAATCCTACCAC 59.541 45.833 0.00 0.00 35.73 4.16
5950 6302 4.508405 CCCTTGACCTTCAAAATCCTACCA 60.508 45.833 0.00 0.00 35.73 3.25
6005 6361 4.762251 AGAAGGGCAAGAAGTCAATGTAAC 59.238 41.667 0.00 0.00 0.00 2.50
6195 6557 2.972625 TGTAAAGGATGGAGCTTGTCG 58.027 47.619 0.00 0.00 0.00 4.35
6208 6570 9.162764 ACAAATAGCTGTAACTGTATGTAAAGG 57.837 33.333 0.00 0.00 0.00 3.11
6214 6576 9.849607 CGAATAACAAATAGCTGTAACTGTATG 57.150 33.333 0.00 0.00 0.00 2.39
6215 6577 9.595823 ACGAATAACAAATAGCTGTAACTGTAT 57.404 29.630 0.00 0.00 0.00 2.29
6216 6578 8.991243 ACGAATAACAAATAGCTGTAACTGTA 57.009 30.769 0.00 0.00 0.00 2.74
6217 6579 7.900782 ACGAATAACAAATAGCTGTAACTGT 57.099 32.000 0.00 0.00 0.00 3.55
6218 6580 9.849607 CATACGAATAACAAATAGCTGTAACTG 57.150 33.333 0.00 0.00 0.00 3.16
6219 6581 9.042008 CCATACGAATAACAAATAGCTGTAACT 57.958 33.333 0.00 0.00 0.00 2.24
6221 6583 9.602568 TTCCATACGAATAACAAATAGCTGTAA 57.397 29.630 0.00 0.00 0.00 2.41
6222 6584 9.256477 CTTCCATACGAATAACAAATAGCTGTA 57.744 33.333 0.00 0.00 0.00 2.74
6223 6585 7.985184 TCTTCCATACGAATAACAAATAGCTGT 59.015 33.333 0.00 0.00 0.00 4.40
6239 6601 5.069251 ACAGGGTCTAAGATTCTTCCATACG 59.931 44.000 1.27 0.00 0.00 3.06
6241 6603 6.672218 TGAACAGGGTCTAAGATTCTTCCATA 59.328 38.462 1.27 0.00 0.00 2.74
6249 6611 6.671779 AGAGATTCTGAACAGGGTCTAAGATT 59.328 38.462 1.93 0.00 0.00 2.40
6257 6619 4.360889 AGATGAGAGATTCTGAACAGGGT 58.639 43.478 1.93 0.00 0.00 4.34
6260 6622 4.609947 CGGAGATGAGAGATTCTGAACAG 58.390 47.826 0.00 0.00 0.00 3.16
6261 6623 3.181482 GCGGAGATGAGAGATTCTGAACA 60.181 47.826 0.00 0.00 0.00 3.18
6266 6628 1.879380 CGAGCGGAGATGAGAGATTCT 59.121 52.381 0.00 0.00 0.00 2.40
6268 6630 1.606668 GTCGAGCGGAGATGAGAGATT 59.393 52.381 0.00 0.00 0.00 2.40
6269 6631 1.202758 AGTCGAGCGGAGATGAGAGAT 60.203 52.381 0.00 0.00 0.00 2.75
6272 6634 0.816018 GGAGTCGAGCGGAGATGAGA 60.816 60.000 0.00 0.00 0.00 3.27
6276 6638 3.587933 GCGGAGTCGAGCGGAGAT 61.588 66.667 0.00 0.00 39.00 2.75
6283 6645 4.544689 CAGCTCCGCGGAGTCGAG 62.545 72.222 45.36 31.30 43.70 4.04
6286 6648 4.803426 CCACAGCTCCGCGGAGTC 62.803 72.222 45.36 37.30 43.70 3.36
6298 6660 2.079925 GGCTAAAACAGAGCTCCACAG 58.920 52.381 10.93 0.49 39.98 3.66
6299 6661 1.608025 CGGCTAAAACAGAGCTCCACA 60.608 52.381 10.93 0.00 39.98 4.17
6300 6662 1.079503 CGGCTAAAACAGAGCTCCAC 58.920 55.000 10.93 0.00 39.98 4.02
6301 6663 0.673644 GCGGCTAAAACAGAGCTCCA 60.674 55.000 10.93 0.00 39.98 3.86
6303 6665 1.003108 GAGCGGCTAAAACAGAGCTC 58.997 55.000 5.27 5.27 43.98 4.09
6306 6668 0.389948 ACGGAGCGGCTAAAACAGAG 60.390 55.000 0.60 0.00 0.00 3.35
6308 6670 0.669318 TCACGGAGCGGCTAAAACAG 60.669 55.000 0.60 0.00 0.00 3.16
6309 6671 0.249953 TTCACGGAGCGGCTAAAACA 60.250 50.000 0.60 0.00 0.00 2.83
6310 6672 0.869730 TTTCACGGAGCGGCTAAAAC 59.130 50.000 0.60 0.00 0.00 2.43
6311 6673 1.595466 TTTTCACGGAGCGGCTAAAA 58.405 45.000 0.60 2.80 0.00 1.52
6313 6675 1.083489 CATTTTCACGGAGCGGCTAA 58.917 50.000 0.60 0.00 0.00 3.09
6314 6676 0.248012 TCATTTTCACGGAGCGGCTA 59.752 50.000 0.60 0.00 0.00 3.93
6315 6677 1.003839 TCATTTTCACGGAGCGGCT 60.004 52.632 0.00 0.00 0.00 5.52
6316 6678 1.425428 CTCATTTTCACGGAGCGGC 59.575 57.895 0.00 0.00 0.00 6.53
6317 6679 1.425428 GCTCATTTTCACGGAGCGG 59.575 57.895 0.00 0.00 43.83 5.52
6320 6682 1.159285 TGCAGCTCATTTTCACGGAG 58.841 50.000 0.00 0.00 0.00 4.63
6321 6683 1.266718 GTTGCAGCTCATTTTCACGGA 59.733 47.619 0.00 0.00 0.00 4.69
6323 6685 1.666888 GGGTTGCAGCTCATTTTCACG 60.667 52.381 0.00 0.00 0.00 4.35
6325 6687 0.597568 CGGGTTGCAGCTCATTTTCA 59.402 50.000 0.00 0.00 0.00 2.69
6326 6688 0.109132 CCGGGTTGCAGCTCATTTTC 60.109 55.000 0.00 0.00 0.00 2.29
6329 6691 1.675641 GACCGGGTTGCAGCTCATT 60.676 57.895 6.32 0.00 0.00 2.57
6331 6693 4.329545 GGACCGGGTTGCAGCTCA 62.330 66.667 6.32 0.00 0.00 4.26
6350 6712 0.250234 TCCTCAATTGTGCTCCGGAG 59.750 55.000 27.83 27.83 0.00 4.63
6351 6713 0.250234 CTCCTCAATTGTGCTCCGGA 59.750 55.000 2.93 2.93 0.00 5.14
6352 6714 1.372087 GCTCCTCAATTGTGCTCCGG 61.372 60.000 5.13 0.00 0.00 5.14
6353 6715 1.699656 CGCTCCTCAATTGTGCTCCG 61.700 60.000 5.13 1.20 0.00 4.63
6354 6716 1.372087 CCGCTCCTCAATTGTGCTCC 61.372 60.000 5.13 0.00 0.00 4.70
6357 6719 0.391661 TCTCCGCTCCTCAATTGTGC 60.392 55.000 5.13 5.54 0.00 4.57
6358 6720 1.649664 CTCTCCGCTCCTCAATTGTG 58.350 55.000 5.13 2.61 0.00 3.33
6359 6721 0.539051 CCTCTCCGCTCCTCAATTGT 59.461 55.000 5.13 0.00 0.00 2.71
6360 6722 0.826715 TCCTCTCCGCTCCTCAATTG 59.173 55.000 0.00 0.00 0.00 2.32
6361 6723 1.208293 GTTCCTCTCCGCTCCTCAATT 59.792 52.381 0.00 0.00 0.00 2.32
6362 6724 0.827368 GTTCCTCTCCGCTCCTCAAT 59.173 55.000 0.00 0.00 0.00 2.57
6364 6726 1.682684 GGTTCCTCTCCGCTCCTCA 60.683 63.158 0.00 0.00 0.00 3.86
6366 6728 2.756283 CGGTTCCTCTCCGCTCCT 60.756 66.667 0.00 0.00 41.48 3.69
6370 6732 2.506438 CGTTCGGTTCCTCTCCGC 60.506 66.667 0.00 0.00 46.49 5.54
6373 6735 2.125633 GCCCGTTCGGTTCCTCTC 60.126 66.667 10.36 0.00 0.00 3.20
6374 6736 2.603776 AGCCCGTTCGGTTCCTCT 60.604 61.111 10.36 0.00 0.00 3.69
6377 6739 0.459759 CTAAGAGCCCGTTCGGTTCC 60.460 60.000 10.36 0.00 42.76 3.62
6378 6740 0.245813 ACTAAGAGCCCGTTCGGTTC 59.754 55.000 10.36 7.52 42.10 3.62
6379 6741 1.549203 TACTAAGAGCCCGTTCGGTT 58.451 50.000 10.36 0.84 0.00 4.44
6380 6742 1.407979 CATACTAAGAGCCCGTTCGGT 59.592 52.381 10.36 0.00 0.00 4.69
6381 6743 1.269621 CCATACTAAGAGCCCGTTCGG 60.270 57.143 4.08 4.08 0.00 4.30
6382 6744 1.679680 TCCATACTAAGAGCCCGTTCG 59.320 52.381 0.00 0.00 0.00 3.95
6383 6745 3.814005 TTCCATACTAAGAGCCCGTTC 57.186 47.619 0.00 0.00 0.00 3.95
6384 6746 4.900054 ACTATTCCATACTAAGAGCCCGTT 59.100 41.667 0.00 0.00 0.00 4.44
6385 6747 4.481072 ACTATTCCATACTAAGAGCCCGT 58.519 43.478 0.00 0.00 0.00 5.28
6386 6748 5.944599 TCTACTATTCCATACTAAGAGCCCG 59.055 44.000 0.00 0.00 0.00 6.13
6387 6749 6.127563 GCTCTACTATTCCATACTAAGAGCCC 60.128 46.154 9.31 0.00 39.07 5.19
6388 6750 6.661805 AGCTCTACTATTCCATACTAAGAGCC 59.338 42.308 15.28 1.28 44.01 4.70
6389 6751 7.413657 CGAGCTCTACTATTCCATACTAAGAGC 60.414 44.444 12.85 11.94 43.50 4.09
6390 6752 7.820386 TCGAGCTCTACTATTCCATACTAAGAG 59.180 40.741 12.85 0.00 0.00 2.85
6391 6753 7.677892 TCGAGCTCTACTATTCCATACTAAGA 58.322 38.462 12.85 0.00 0.00 2.10
6398 6760 5.126384 GCCTATTCGAGCTCTACTATTCCAT 59.874 44.000 12.85 0.00 0.00 3.41
6404 6766 3.397849 TCGCCTATTCGAGCTCTACTA 57.602 47.619 12.85 0.00 34.09 1.82
6450 6812 9.520204 CCCAAACTATTGCTAATAATTGACAAG 57.480 33.333 0.00 0.00 35.10 3.16
6502 6866 4.024302 CGTCATCATCCGTAGTAGCAACTA 60.024 45.833 0.00 0.00 37.15 2.24
6524 6888 2.438434 GGCCAGTCCCCATCAACG 60.438 66.667 0.00 0.00 0.00 4.10
6627 6992 4.974368 ACGTTCACAAAACTTCCATTCA 57.026 36.364 0.00 0.00 0.00 2.57
6654 7019 3.139077 AGTGGTTGGTCTTTCAACGATC 58.861 45.455 0.00 0.00 45.66 3.69
6655 7020 3.208747 AGTGGTTGGTCTTTCAACGAT 57.791 42.857 0.00 0.00 45.66 3.73
6660 7025 4.764050 TTCACTAGTGGTTGGTCTTTCA 57.236 40.909 22.48 0.00 0.00 2.69


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.